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Background <p>The Poaceae is one of the world’s most ecologically and economically important plant families, encompassing major food crops and forage grasses. Despite its agricultural significance, systematic analyses of chloroplast genome evolution across this diverse family remain limited. To understand adaptive evolution in Poaceae species and their phylogenetic relationships, analysis of codon usage and evolutionary pressure in chloroplast genomes is essential. We conducted a comprehensive comparative analysis of 48 Poaceae chloroplast genomes to elucidate codon usage mechanisms and phylogenetic relationships.</p> Results <p>Our analysis revealed consistent codon usage bias across all species. Notably, 93.1% of preferred codons are A/U-ending, indicating the presence of strong compositional constraints. Chloroplast genomes ranged from 129,095 bp to 148,617 bp, with GC content ranging between 38.16% and 39.04%. The average GC content was 38.5%, with GC<sub>3</sub> content (30.51%) significantly lower than GC<sub>1</sub> (47.34%) and GC<sub>2</sub> (39.64%) contents. ENC-GC3s plots, PR2 analysis, and neutrality plot analyses consistently demonstrated that natural selection, rather than mutational pressure, predominantly drives codon usage patterns. Simple sequence repeats (SSRs) analysis showed non-random distribution, with the highest density in intergenic regions (52.6%), followed by introns (28.2%) and coding sequences (19.2%). Mononucleotide and octanucleotide repeats constituted the predominant SSR types. Ka/Ks analysis revealed that 94.67% of chloroplast genes undergo purifying selection (Ka/Ks &lt; 0.5), with photosystem and ribosomal protein genes under the most stringent constraints. Phylogenetic analysis confirmed robust evolutionary relationships, with genome synteny strongly correlating with taxonomic classification.</p> Conclusion <p>This study provides the most comprehensive analysis of Poaceae chloroplast genome evolution to date, revealing selection-driven codon optimization that balances functional conservation with adaptive flexibility. The predominance of purifying selection reflects the critical importance of chloroplast gene function, while SSR distribution patterns suggest roles in genome plasticity and regulatory functions. These findings deepen our understanding of grass evolution and provide valuable resources for molecular marker development, phylogenetic studies, and crop improvement programs addressing global food security challenges.</p>

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Comprehensive analysis of chloroplast genome evolution in Poaceae: codon usage patterns, selection pressures, and phylogenomic relationships

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月27日

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  • Xiaohe Geng,
  • Ying Xue,
  • Haodi Wang,
  • Hao Tu,
  • Rui Jing,
  • Zixiong Li,
  • Yunpeng Gai

摘要

Background

The Poaceae is one of the world’s most ecologically and economically important plant families, encompassing major food crops and forage grasses. Despite its agricultural significance, systematic analyses of chloroplast genome evolution across this diverse family remain limited. To understand adaptive evolution in Poaceae species and their phylogenetic relationships, analysis of codon usage and evolutionary pressure in chloroplast genomes is essential. We conducted a comprehensive comparative analysis of 48 Poaceae chloroplast genomes to elucidate codon usage mechanisms and phylogenetic relationships.

Results

Our analysis revealed consistent codon usage bias across all species. Notably, 93.1% of preferred codons are A/U-ending, indicating the presence of strong compositional constraints. Chloroplast genomes ranged from 129,095 bp to 148,617 bp, with GC content ranging between 38.16% and 39.04%. The average GC content was 38.5%, with GC3 content (30.51%) significantly lower than GC1 (47.34%) and GC2 (39.64%) contents. ENC-GC3s plots, PR2 analysis, and neutrality plot analyses consistently demonstrated that natural selection, rather than mutational pressure, predominantly drives codon usage patterns. Simple sequence repeats (SSRs) analysis showed non-random distribution, with the highest density in intergenic regions (52.6%), followed by introns (28.2%) and coding sequences (19.2%). Mononucleotide and octanucleotide repeats constituted the predominant SSR types. Ka/Ks analysis revealed that 94.67% of chloroplast genes undergo purifying selection (Ka/Ks < 0.5), with photosystem and ribosomal protein genes under the most stringent constraints. Phylogenetic analysis confirmed robust evolutionary relationships, with genome synteny strongly correlating with taxonomic classification.

Conclusion

This study provides the most comprehensive analysis of Poaceae chloroplast genome evolution to date, revealing selection-driven codon optimization that balances functional conservation with adaptive flexibility. The predominance of purifying selection reflects the critical importance of chloroplast gene function, while SSR distribution patterns suggest roles in genome plasticity and regulatory functions. These findings deepen our understanding of grass evolution and provide valuable resources for molecular marker development, phylogenetic studies, and crop improvement programs addressing global food security challenges.